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miic (version 1.0)

Multivariate Information Inductive Causation

Description

We report an information-theoretic method which learns a large class of causal or non-causal graphical models from purely observational data, while including the effects of unobserved latent variables, commonly found in many datasets. Starting from a complete graph, the method iteratively removes dispensable edges, by uncovering significant information contributions from indirect paths, and assesses edge-specific confidences from randomization of available data. The remaining edges are then oriented based on the signature of causality in observational data. This approach can be applied on a wide range of datasets and provide new biological insights on regulatory networks from single cell expression data, genomic alterations during tumor development and co-evolving residues in protein structures. For more information you can refer to: Verny et al. Plos Comput Biol. (2017) .

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Version

Install

install.packages('miic')

Monthly Downloads

265

Version

1.0

License

GPL (>= 2)

Maintainer

Nadir Sella

Last Published

November 22nd, 2017

Functions in miic (1.0)

miic

MIIC, causal network learning algorithm including latent variables
hematoData

Early blood development: single cell binary gene expression data
miic.evaluate.effn

Evaluate the effective number of samples
ohno

Tetraploidization in vertebrate evolution
miic.plot

Igraph plotting function for miic
ohno_stateOrder

Tetraploidization in vertebrate evolution
cosmicCancer

Genomic and ploidy alterations in breast tumors
miic.write.style.cytoscape

Style writing function for the miic network
cosmicCancer_stateOrder

Genomic and ploidy alterations in breast tumors
miic.write.network.cytoscape

Graphml writing function for the miic graph